Bacterial microcompartments are proteinaceous complexes that catalyze metabolic pathways in a manner reminiscent of organelles. Although microcompartment structure is well understood, much less is known about their assembly and function in vivo. We show here that carboxysomes, CO(2)-fixing microcompartments encoded by 10 genes, can be heterologously produced in Escherichia coli. Expression of carboxysomes in E. coli resulted in the production of icosahedral complexes similar to those from the native host. In vivo, the complexes were capable of both assembling with carboxysomal proteins and fixing CO(2). Characterization of purified synthetic carboxysomes indicated that they were well formed in structure, contained the expected molecular components, and were capable of fixing CO(2) in vitro. In addition, we verify association of the postulated pore-forming protein CsoS1D with the carboxysome and show how it may modulate function. We have developed a genetic system capable of producing modular carbon-fixing microcompartments in a heterologous host. In doing so, we lay the groundwork for understanding these elaborate protein complexes and for the synthetic biological engineering of self-assembling molecular structures.
Members of the rhizobia are distinguished for their ability to establish a nitrogen-fixing symbiosis with leguminous plants. While many details of this relationship remain a mystery, much effort has gone into elucidating the mechanisms governing bacterium-host recognition and the events leading to symbiosis. Several signal molecules, including plant-produced flavonoids and bacterially produced nodulation factors and exopolysaccharides, are known to function in the molecular conversation between the host and the symbiont. Work by several laboratories has shown that an additional mode of regulation, quorum sensing, intercedes in the signal exchange process and perhaps plays a major role in preparing and coordinating the nitrogen-fixing rhizobia during the establishment of the symbiosis. Rhizobium leguminosarum, for example, carries a multitiered quorum-sensing system that represents one of the most complex regulatory networks identified for this form of gene regulation. This review focuses on the recent stream of information regarding quorum sensing in the nitrogen-fixing rhizobia. Seminal work on the quorum-sensing systems of R. leguminosarum bv. viciae, R. etli, Rhizobium sp. strain NGR234, Sinorhizobium meliloti, and Bradyrhizobium japonicum is presented and discussed. The latest work shows that quorum sensing can be linked to various symbiotic phenomena including nodulation efficiency, symbiosome development, exopolysaccharide production, and nitrogen fixation, all of which are important for the establishment of a successful symbiosis. Many questions remain to be answered, but the knowledge obtained so far provides a firm foundation for future studies on the role of quorum-sensing mediated gene regulation in host-bacterium interactions.
This paper reports on a study of recent Antitrust Division horizontal price fixing cases. The objective of the study was to determine if there has been a specific set of characteristics associated with the product or product markets that have been the subjects of price fixing. If such a pattern exists, it might provide empirical insight into some aspects of oligopoly behavior. From a policy point of view, any pattern that is found could be used in a positive enforcement program designed to investigate the "most likely" areas of price fixing. Section I reviews the academic literature which has dealt with the problem of horizontal conspiracy; Section II describes the sample and the methodology used in the study; and Section III summarizes the results.
Bacteria belonging to the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium (collectively referred to as rhizobia) grow in the soil as free-living organisms but can also live as nitrogen-fixing symbionts inside root nodule cells of legume plants. The interactions between several rhizobial species and their host plants have become models for this type of nitrogen-fixing symbiosis. Temperate legumes such as alfalfa, pea, and vetch form indeterminate nodules that arise from root inner and middle cortical cells and grow out from the root via a persistent meristem. During the formation of functional indeterminate nodules, symbiotic bacteria must gain access to the interior of the host root. To get from the outside to the inside, rhizobia grow and divide in tubules called infection threads, which are composite structures derived from the two symbiotic partners. This review focuses on symbiotic infection and invasion during the formation of indeterminate nodules. It summarizes root hair growth, how root hair growth is influenced by rhizobial signaling molecules, infection of root hairs, infection thread extension down root hairs, infection thread growth into root tissue, and the plant and bacterial contributions necessary for infection thread formation and growth. The review also summarizes recent advances concerning the growth dynamics of rhizobial populations in infection threads.
Genomic traces of symbiosis loss A symbiosis between certain bacteria and their plant hosts delivers fixed nitrogen to the plants. Griesmann et al. sequenced several plant genomes to analyze why nitrogen-fixing symbiosis is irregularly scattered through the evolutionary tree (see the Perspective by Nagy). Various genomes carried traces of lost pathways that could have supported nitrogen-fixing symbiosis. It seems that this symbiosis, which relies on multiple pathways and complex interorganismal signaling, is susceptible to selection and prone to being lost over evolutionary time. Science , this issue p. eaat1743 ; see also p. 125
The problem of automatically fixing programming errors is a very active research topic in software engineering. This is a challenging problem as fixing even a single error may require analysis of the entire program. In practice, a number of errors arise due to programmer's inexperience with the programming language or lack of attention to detail. We call these common programming errors. These are analogous to grammatical errors in natural languages. Compilers detect such errors, but their error messages are usually inaccurate. In this work, we present an end-to-end solution, called DeepFix, that can fix multiple such errors in a program without relying on any external tool to locate or fix them. At the heart of DeepFix is a multi-layered sequence-to-sequence neural network with attention which is trained to predict erroneous program locations along with the required correct statements. On a set of 6971 erroneous C programs written by students for 93 programming tasks, DeepFix could fix 1881 (27%) programs completely and 1338 (19%) programs partially.
In agroecosystems, nitrogen is one of the major nutrients limiting plant growth. To meet the increased nitrogen demand in agriculture, synthetic fertilizers have been used extensively in the latter part of the twentieth century, which have led to environmental challenges such as nitrate pollution. Biological nitrogen fixation (BNF) in plants is an essential mechanism for sustainable agricultural production and healthy ecosystem functioning. BNF by legumes and associative, endosymbiotic, and endophytic nitrogen fixation in non-legumes play major roles in reducing the use of synthetic nitrogen fertilizer in agriculture, increased plant nutrient content, and soil health reclamation. This review discusses the process of nitrogen-fixation in plants, nodule formation, the genes involved in plant-rhizobia interaction, and nitrogen-fixing legume and non-legume plants. This review also elaborates on current research efforts involved in transferring nitrogen-fixing mechanisms from legumes to non-legumes, especially to economically important crops such as rice, maize, and wheat at the molecular level and relevant other techniques involving the manipulation of soil microbiome for plant benefits in the non-legume root environment.
Abstract Anti‐complement immunofluorescence (ACIF) was used to study the complementfixing antigens of human lymphoblastoid cell lines. These cell lines carry the Epstein‐Barr virus (EBV) genome although only producer cultures synthetize EBV‐specific antigens (virus capsid antigen, VCA and early antigen, EA) detectable by direct and indirect immunofluorescence, usually in less than 5% of the cells. The ACIF test revealed an antigen localized in the nucleus of the lymphoblastoid cells. In contrast to EA and VCA, this antigen was present in over 90% of the cells of both producer and non‐producer cultures. The antigen was shown to be specific for EBV by comparing the reactions of 52 sera in the ACIF test. Sera giving the nuclear reaction contained antibodies to VCA, EA or antigens detectable by complement fixation tests on cell extracts, but sera without EBV antibodies failed to give the reaction. Weak, equivocal or discordant reactions occurred with six sera with low titres in VCA, EA or complement fixation tests. Cell lines derived by transformation of human and primate lymphocytes by EBV gave the nuclear reaction. Control cells with no known association with EBV were non‐reactive. These included foetal lymphocytes transformed by phytohaemagglutinin, cell lines derived from breast cancer, glioma, normal glia, pleuritis maligna and myeloma, and two marmoset lymphoid lines carrying Herpesvirus saimiri (HVS). In preliminary experiments, the ACIF test was used as a tool to trace the EBV genome at the cellular level. Cells from two Burkitt lymphoma biopsies, one tested after biopsy and one after passaging in nude mice, contained an EBV‐specific antigen. Three clones of cells derived from hybrids of mouse somatic cells and a human lymphoblastoid cell line also contained such an antigen, but the number of reactive cells varied from clone to clone. A fourth clone was non‐reactive.
Azospirillum represents the best characterized genus of plant growth-promoting rhizobacteria. Other free-living diazotrophs repeatedly detected in association with plant roots, include Acetobacter diazotrophicus, Herbaspirillum seropedicae, Azoarcus spp. and Azotobacter. Four aspects of the Azospirillum-plant root interaction are highlighted: natural habitat, plant root interaction, nitrogen fixation and biosynthesis of plant growth hormones. Each of these aspects is dealt with in a comparative way. Azospirilla are predominantly surface-colonizing bacteria, whereas A. diazotrophicus, H. seropedicae and Azoarcus sp. are endophytic diazotrophs. The attachment of Azospirillum cells to plant roots occurs in two steps. The polar flagellum, of which the flagellin was shown to be a glycoprotein, mediates the adsorption step. An as yet unidentified surface polysaccharide is believed to be essential in the subsequent anchoring phase. In Azoarcus sp. the attachment process is mediated by type IV pili. Nitrogen fixation structural genes (nif) are highly conserved among all nitrogen-fixing bacteria, and in all diazotrophic species of the class of proteobacteria examined, the transcriptional activator NifA is required for expression of other nif genes in response to two major environmental signals (oxygen and fixed N). However, the mechanisms involved in this control can vary in different organisms. In Azospirillum brasilense and H. seropedicae (alpha- and beta-subgroup, respectively), NifA is inactive in conditions of excess nitrogen. Activation of NifA upon removal of fixed N seems to involve, either directly or indirectly, the signal transduction protein P(II). The presence of four conserved cysteine residues in the NifA protein might be an indication that NifA is directly sensitive to oxygen. In Azotobacter vinelandii (gamma-subgroup) nifA is cotranscribed with a second gene nifL. The nifL gene product inactivates NifA in response to high oxygen tension and cellular nitrogen-status. NifL was found to be a redox-sensitive flavoprotein. The relief of NifL inhibition on NifA activity, in response to N-limitation, is suggested to involve a P(II)-like protein. Moreover, nitrogenase activity is regulated according to the intracellular nitrogen and O(2) level. In A. brasilense and Azospirillum lipoferum posttranslational control of nitrogenase, in response to ammonium and anaerobiosis, involves ADP-ribosylation of the nitrogenase iron protein, mediated by the enzymes DraT and DraG. At least three pathways for indole-3-acetic acid (IAA) biosynthesis in A. brasilense exist: two Trp-dependent (the indole-3-pyruvic acid and presumably the indole-3-acetamide pathway) and one Trp-independent pathway. The occurrence of an IAA biosynthetic pathway not using Trp (tryptophan) as precursor is highly unusual in bacteria. Nevertheless, the indole-3-pyruvate decarboxylase encoding ipdC gene is crucial in the overall IAA biosynthesis in Azospirillum. A number of genes essential for Trp production have been isolated in A. brasilense, including trpE(G) which codes for anthranilate synthase, the key enzyme in Trp biosynthesis. The relevance of each of these four aspects for plant growth promotion by Azospirillum is discussed.
Many countries are pursuing innovation-led “smart” growth, which requires long-run strategic investments and public policies that aim to create and shape markets, rather than just “fixing” markets or systems. Market creation has characterized the kind of mission-oriented investments that led to putting a man on the moon and are currently galvanizing green innovation. Mission-oriented innovation has required public agencies to not only “de-risk” the private sector, but also to lead the direct creation of new technological opportunities and market landscapes. This paper considers four key issues that arise from a market-creating framework for policy: (1) decision-making on the direction of change; (2) the nature of (public and private) organizations that can welcome the underlying uncertainty and discovery process; (3) the evaluation of mission-oriented and market-creation policies; and (4) the ways in which both risks and rewards can be shared so that smart growth can also result in inclusive growth.
Today between forty and sixty nations, home to more than one billion people, have either collapsed or are teetering on the brink of failure. The world's worst problems-terrorism, drugs and human trafficking, absolute poverty, ethnic conflict, disease, genocide-originate in such states, and the international community has devoted billions of dollars to solving the problem. Yet by and large the effort has not succeeded. Ashraf Ghani and Clare Lockhart have taken an active part in the effort to save failed states for many years, serving as World Bank officials, as advisers to the UN, and as high-level participants in the new government of Afghanistan. In Fixing Failed States, they describe the issue-vividly and convincingly-offering an on-the-ground picture of why past efforts have not worked and advancing a groundbreaking new solution to this most pressing of global crises. For the paperback edition, they have added a new preface that addresses the continuing crisis in light of ongoing governance problems in weak states like Afghanistan and the global financial recession. As they explain, many of these countries already have the resources they need, if only we knew how to connect them to global knowledge and put them to work in the right way. Their state-building strategy, which assigns responsibility equally among the international community, national leaders, and citizens, maps out a clear path to political and economic stability. The authors provide a practical framework for achieving these ends, supporting their case with first-hand examples of struggling territories such as Afghanistan, Sudan, Kosovo and Nepal as well as the world's success stories-Singapore, Ireland, and even the American South.
<italic>Fixing Language</italic> is a book about ways in which language (and other representational devices) can be defective and improved. In all parts of philosophy there are philosophers who criticize the concepts we have and propose ways to improve them. Once one notices this about philosophy, it’s easy to see that revisionist projects occur in a range of other intellectual disciplines and in ordinary life. That fact gives rise to a cluster of questions: How does the process of conceptual amelioration work? What are the limits of revision (how much revision is too much)? How does the process of revision fit into an overall theory of language and communication? This book is an effort to answer those questions. In so doing, it is also an attempt to draw attention to a tradition in twentieth- and twenty-first-century philosophy that isn’t sufficiently recognized as a unified tradition. There’s a straight intellectual line from Frege (e.g. of the <italic>Begriffsschrift</italic>) and Carnap to a cluster of contemporary work that isn’t typically seen as closely related: much work on gender and race, revisionism about truth, revisionists about moral language, and revisionists in metaphysics and philosophy of mind. These views all have common core commitments: revision is both possible and important. They also face common challenges: how is amelioration done, what assumptions need to be made, e.g., about the nature of concepts, and what are the limits of revision?
Isolated soil DNA from an oak-hornbeam forest close to Cologne, Germany, was suitable for PCR amplification of gene segments coding for the 16S rRNA and nitrogenase reductase (NifH), nitrous oxide reductase (NosZ), cytochrome cd(1)-containing nitrite reductase (NirS), and Cu-containing nitrite reductase (NirK) of denitrification. For each gene segment, diverse PCR products were characterized by cloning and sequencing. None of the 16S rRNA gene sequences was identical to any deposited in the data banks, and therefore each of them belonged to a noncharacterized bacterium. In contrast, the analyzed clones of nifH gave only a few different sequences, which occurred many times, indicating a low level of species richness in the N2-fixing bacterial population in this soil. Identical nifH sequences were also detected in PCR amplification products of DNA of a soil approximately 600 km distant from the Cologne area. Whereas biodiversity was high in the case of nosZ, only a few different sequences were obtained with nirK. With respect to nirS, cloning and sequencing of the PCR products revealed that many false gene segments had been amplified with DNA from soil but not from cultured bacteria. With the 16S rRNA gene data, many sequences of uncultured bacteria belonging to the Acidobacterium phylum and actinomycetes showed up in the PCR products when isolated DNA was used as the template, whereas sequences obtained for nifH and for the denitrification genes were closely related to those of the proteobacteria. Although in such an experimental approach one has to cope with the enormous biodiversity in soils and only a few PCR products can be selected at random, the data suggest that denitrification and N2 fixation are not genetic traits of most of the uncultured bacteria.
Colonies of the Caribbean coral Montastraea cavernosa exhibit a solar-stimulated orange-red fluorescence that is spectrally similar to a variety of fluorescent proteins expressed by corals. The source of this fluorescence is phycoerythrin in unicellular, nonheterocystis, symbiotic cyanobacteria within the host cells of the coral. The cyanobacteria coexist with the symbiotic dinoflagellates (zooxanthellae) of the coral and express the nitrogen-fixing enzyme nitrogenase. The presence of this prokaryotic symbiont in a nitrogen-limited zooxanthellate coral suggests that nitrogen fixation may be an important source of this limiting element for the symbiotic association.
Abstract ‘Fixing the Economy’, shows how the modern understanding of ‘the economy’ as the totality of the relations of production, distribution and consumption of goods and services within a given country or region arose in a mid-twentieth-century crisis of economic representation. The economy, represented as an autonomous domain, participated in the (largely post-Second World War) re-imagining of the nation-state and the postcolonial international order, and provided a concept of development without political upheaval. In considering the economic life of an Egyptian village, however, Mitchell demonstrates that market and domestic production and consumption are irreducibly hybrid and that the practical foundations of the economy as representation make it impossible any longer to see its imagined referent as the very type of the non-discursive and the material. Keywords: Economy Economics Keynes Representation Agriculture Households Water Buffalo
Based on a groundbreaking theory of crime prevention, this practical and empowering book shows how citizens, business owners, and police can work together to ensure the safety of their George Kelling, one of America s leading criminologists, has proven the success of his method across the country, from the New York City subways to the public parks of Seattle. Here, Kelling and urban anthropologist and lawyer Catherine Coles demonstrate that by controlling disorderly behavior in public spaces, we can create an environment where serious crime cannot flourish, and they explain how to adapt these effective methods for use in our own homes and communities.
We note that common implementations of adaptive gradient algorithms, such as Adam, limit the potential benefit of weight decay regularization, because the weights do not decay multiplicatively (as would be expected for standard weight decay) but by an additive constant factor. We propose a simple way to resolve this issue by decoupling weight decay and the optimization steps taken w.r.t. the loss function. We provide empirical evidence that our proposed modification (i) decouples the optimal choice of weight decay factor from the setting of the learning rate for both standard SGD and Adam, and (ii) substantially improves Adam's generalization performance, allowing it to compete with SGD with momentum on image classification datasets (on which it was previously typically outperformed by the latter). We also demonstrate that longer optimization runs require smaller weight decay values for optimal results and introduce a normalized variant of weight decay to reduce this dependence. Finally, we propose a version of Adam with warm restarts (AdamWR) that has strong anytime performance while achieving state-of-the-art results on CIFAR-10 and ImageNet32x32. Our source code will become available after the review process.
暂无摘要（点击查看原文获取完整内容）
暂无摘要（点击查看原文获取完整内容）
The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by Göttfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.